dme-mir-4949- 12- and 20-way alignments

dme-mir-4949	chr3R:27044995-27045094 -	Known_mirbase
[View on miRBase]	[View on UCSC Genome Browser {Cornell Mirror}]	five_prime_UTR

Legend:

   mature strand at position 27045012-27045033
   star strand at position 27045055-27045075
   mutations
   read mismatches
   coordinate mismatch (possible incorrect ortholog)

12-way Fast Statistical Aligner re-alignment (From MAFs)

Species	Coordinate	Alignment
dm3	chr3R:27044980-27045109 -	TGCG----------AAACGT----------------GTTTGATAATGCG---CCGCCATCTTGCGGCACACTCGCACACA----CACA----------------------------CGTGTGCCA------------------TTCTGGTTTTGCAGTGGTGTGCGTGTGT-----GCCTC----GAGTCGTTGCGTCACTGGAAA---AGTTA-----------GAAAATC
droSim1	chr3R:26688146-26688275 -	TGCG----------AAACGT----------------GTTTGATAATGCG---CCGCCATCTTGCGGCACACTCGCACACA----CACA----------------------------CGTGTGCCA------------------GGCTGGTTTTGCAGTGGTGTGCGTGTGT-----GCCTC----GAGTCGTTGCGTCACTGGAAA---AGTTA-----------GAAAATC
droSec1	super_4:5862973-5863106 -	TGCG----------AAACGT----------------GTTTGATAATGCG---CCGCCATCTTGCGGCACACTCGCACACACACACACA----------------------------CGTGTGCCA------------------GGCTGGTTTTGCAGTGGTTTGCGTGTGT-----GCCTC----AAGTCGTTGCGTCACTGAAAA---AGTTA-----------GAAAATC
droYak2	chr3R:27981306-27981430 -	TGCG----------AAACGT----------------GTTTGAAAATCCG---TCGCCATCTTGCGGCACACTCA--CACA----CACA----------------------------CGTGTGCCA------------------ATATGGTT-TGCAGTGGTGTGCGTGTG-------CCTC----GAGTCGTTGCGTCACTGGAAA---AGTCA-----------GAAAATC
droEre2	scaffold_4820:935924-936048 +	TGCA----------AAACGT----------------GTTGGAAAATTCG---CCGCCATCTTGCGGCACACACA----CA----CACA----------------------------CGTGTGCCA------------------GTCTGGTT-TGCAGTGGTGTGCGTGTGG-----GCCTC----GAGTCGTTGCGTCACTGGAAA---AGTCC-----------GAAAATC
droAna3	scaffold_13340:14436299-14436405 -	CTCA----------AAACGT----------------GTTCAA-----TGGAATCGCCATCTTGCGGCTCACACA----------CACA------------------------------TGTG-------------------------------ACAGTTGTTCGTGCGTGT-----GTCTGG---GAGTCGTTGCGTCACTGAGAA---AGTCG-----------GAAAAT-
dp4	chr2:85296-85449 +	TGTA---------------CATTTTCTCGAAAACGTGTCGAA-----TG---TCGCCATCTTGCGGgt-gtgtgtgtGtg----tgtg----------------------------tgtgtgtTGTGACGAGAGGAATTGCCAGTGCT------CAATAGTGTGCCTGTGT-----G--TC----GAGACGTTGCGTCACTGAAAA---AGTCGAACAGC--AAAGTAAATT
droPer1	super_7:2877004-2877157 +	TGTA---------------CATTTTCTCGAAAACGTGTCGAA-----TG---TCGCCATCTTGCGGgt-gtgtgtgtGtg----tgtg----------------------------tgtgtgtTGTGACGAGAGGAATTGCCAGTGCT------CAATAGTGTGCCTGTGT-----G--TC----GAGACGTTGCGTCACTGAAAA---AGTCGAACAGC--AAAGTAAATT
droWil1	scaffold_181108:712012-712143 -	TGAA----------AAATGTATTTTATCT--A--------GAGATATTG---TCGCCATTTTGCGGCACTCACA----------CACA----------------------------CGTGTCACA------AGAGAACTGTCAAA------TTGTAGCTGTATGCGTGAG---------AC----CAGTCGTTGCGTCACAGCAAA---AGTTT-----------TCAAATT
droVir3	scaffold_12855:1227208-1227391 +	ACAG-ATGAGTGAAAATAATATTTTTTCA--AACGTGTTCAG-----TG---TCGCCATCTTGCGGCACATACACACACA----TTCA------G----ACAAGATGTCACACGGAC--GT------ACGAAGAGAACTGTCAGTGTGTTT-------TGTGTGCCGTAGTGTGGAGTGTA----AATTTGTTGCGTCACTAGAAA---AGTTCAACTGT-TGAAGGAAATC
droMoj3	scaffold_6540:26974772-26974936 +	AAAA-ACAAGTGAAAATAACATTTTTTCA--AACGTGTTCAA-----TG---TCGCCATCTTGCGGCTCACGCA--CACA----CTCA------T----GCAAGATGTCACACGGGC--GT------ATGAAGAGAACTGTCAGTGTT------------------ACT-------GTGTG----AAGTCGTTGCGTCACTAGAAA---AGTTCAACGATTTGAAGAAAATT
droGri2	scaffold_14624:3814528-3814714 +	GGAATATTAGTGAAAATATTATTTTCTCC--AACGTGTTCAA---TGTG---TCGCCATCTTGCGGgt-gtTGgtgtgtG----tgtgtgtgtgtgtgtg-tAGATGTCACACGGGCCCGT------ATGAAGAGAACTGTCAGTTT------GTGTCAGTGTGCGTGTG-------CTTT-ACTCTATTGTTGCGTCACAAGAAACTAAAA-----------AAGAAAATC

20-way Fast Statistical Aligner re-alignment (Top LASTZ hits)

Species	Coordinate	Lastz Id	Alignment
dm3	chr3R:27044980-27045109 -	NA	TG-C-------G-------------AAACGTGTTTG-AT---------------------AATGCGCCGCCATCTTGCGGCACACTCGCAC----ACACAC----ACG---TGTG------------------------CCATTCTGGTTTTGC---------AGTGGTGTGCGTGTGTGCCTC-GAGTCGTTGCGTCACTGGAAAAGTTAG-----------AAAATC
droSim1	chr3R:26688146-26688275 -	3	TG-C-------G-------------AAACGTGTTTG-AT---------------------AATGCGCCGCCATCTTGCGGCACACTCGCAC----ACACAC----ACG---TGTG------------------------CCAGGCTGGTTTTGC---------AGTGGTGTGCGTGTGTGCCTC-GAGTCGTTGCGTCACTGGAAAAGTTAG-----------AAAATC
droSec1	super_4:5862973-5863106 -	1	TG-C-------G-------------AAACGTGTTTG-AT---------------------AATGCGCCGCCATCTTGCGGCACACTCGCACACACACA--C--ACACG---TGTG------------------------CCAGGCTGGTTTTGC---------AGTGGTTTGCGTGTGTGCCTC-AAGTCGTTGCGTCACTGAAAAAGTTAG-----------AAAATC
droYak2	chr3R:27981306-27981430 -	1	TG-C-------G-------------AAACGTGTTTG-AA---------------------AATCCGTCGCCATCTTGCGGCACACTCACAC----ACAC------ACG---TGTG------------------------CCAATATGGTT-TGC---------AGTGGTGTGCGTGTGC--CTC-GAGTCGTTGCGTCACTGGAAAAGTCAG-----------AAAATC
droEre2	scaffold_4820:935924-936048 +	3	TG-C-------A-------------AAACGTGTTGG-AA---------------------AATTCGCCGCCATCTTGCGGCACACACACAC----AC--------ACG---TGTG------------------------CCAGTCTGGTT-TGC---------AGTGGTGTGCGTGTGGGCCTC-GAGTCGTTGCGTCACTGGAAAAGTCCG-----------AAAATC
droEug1	scf7180000407010:15842-15967 -	1	TG-C-------C-------------AAACGTGATTA-AT---------------TTCT--AATTTGTCGCCATCTTGCGGCACACACACAC--------------GCA---TGTG------------------------CCTACCAGGTT-TTC---------AGTGGTGTGCGTATGT--CGC-TGGTCGTTGCGTCACTGAAAAAGTCGG----------GAAAAAC
droBia1	scf7180000302113:268003-268130 +	1	TG-C-------G-------------AAACGTGTTTG-AT---------------------AATCCGCCGCCATCTTGCGGCACACTCACAC----ACACAC--GGGCA---TGTG------------------------CCAGCCAGGT--TGC---------GGTGGTGTGCGTGTGT--CCC-GAGTCGTTGCGTCACTGGAAAAGTGGG-----------AAAATC
droTak1	scf7180000415286:165319-165444 -	1	TG-C-------G-------------AAACGTGTTTG-AT---------------------AATCCGTCGCCATCTTGCGGCACACTCACAC----ACACGC--GGGCA---TGTG------------------------CCC-----GT-TTGC---------AGTGGTGTGCGTGTGTGTCTC-GAGTCGTTGCGTCACTGGAAAAGTCGG-----------AAAAAC
droEle1	scf7180000491194:1053105-1053231 -	1	TG-C-------G-------------AAACGTGTTTG-AT---------------------AGTTCGTCGCCATCTTGCGGCACACTTCCAC----ACACAC----ACA---TGTG------------------------CTATTCAGGTT-CTC---------AAAAGTGTGCGTGTGT--GTA-GAGTCGTTGCGTCACTGGAAAAGTCGG-----------AAAAAC
droRho1	scf7180000777206:283291-283415 +	3	TG-C-------G-------------AAACGTGTTTG-AT---------------------AATCCGTCGCCATCTTGCGGCACACTCACAC----ACAC------ACA---TGTG------------------------CCAGTCAGGTT-TTC---------AGTACTGTGCGTGTGT--CTC-GAGTCGTTGCGTCACTGGAAAAGTCGG-----------AAAAAC
droFic1	scf7180000453782:260753-260875 +	1	TG-C-------G-------------AAACGTGTTTG-AT---------------------TATTTGTCGCCATCTTGCGGCACACTGACAC----AC--------ACA---TGTG------------------------CCTTTCAGGTT-TGC---------CCTGGTGTGCGTGTGT--CTC-AAATCGTTGCGTCACTGGAAAAGTCTG-----------AAAAAA
droKik1	scf7180000301923:160273-160394 -	1	TG-C-------G-AAAAGATGAACGAAACGTGCTA--------------------------AATTGTCGCCATCTTGCGGCACACACACAC--------------ACA---TGTG------------------------ACAGA----TT---C---------AG-AGTGTGCGTGTGT--CTC-GAGTCGTTGCGTCACTGAAAAAGTCGG-----------AAAACT
droAna3	scaffold_13340:14436299-14436405 -	2	CT-C-------A-------------AAACGTGTTCA-ATGG-------------------AA----TCGCCATCTTGCGGCTCACACAC----------------ACA---TGTGAC-----------------AGTTGT---------T------------------CGTGCGTGTGT--CTGGGAGTCGTTGCGTCACTGAGAAAGTCGG-----------AAAA-T
droBip1	scf7180000395971:733981-734084 +	1	T--C-------A-------------AAACGTGTTCA-AT---------------------GAATTGTCGCCATCTTGCGGCTCACACAC----------------ACA---TGTG------------------------ACAGT-----T------------------CGTGCGTGTGT--CTG-GAGTCGTTGCGTCACTGAGAAAGTCGG-----------AAAA-T
dp4	chr2:85298-85449 +	1	TA-CATTTTCTCGA-----------AAACGTGTCGA-AT--------------------------GTCGCCATCTTGCGGCACACACACAGACACACA--C--ACACA---TGTGAC----------G-AGAGGAATTGCCA-----GT-GCTC---------AATAGTGTGCCTGTGT--GTC-GAGACGTTGCGTCACTGAAAAAGTCGAACAGC--AAAGTAAATT
droPer1	super_7:2877006-2877157 +	1	TA-CATTTTCTCGA-----------AAACGTGTCGA-AT--------------------------GTCGCCATCTTGCGGCACACACACAGACACACA--C--ACACA---TGTGAC----------G-AGAGGAATTGCCA-----GT-GCTC---------AATAGTGTGCCTGTGT--GTC-GAGACGTTGCGTCACTGAAAAAGTCGAACAGC--AAAGTAAATT
droWil1	scaffold_181108:712012-712143 -	1	TG-A-------A-------------AAATGTATTTT-AT---------------CTAGAGATATTGTCGCCATTTTGCGGCACTCACACAC--------------ACG---TGTCAC----------A-AGA-GAACTGTCA-----AA-TTGT---------AGCTGTATGCGTGAGA----C-CAGTCGTTGCGTCACAGCAAAAGTTTT-----------CAAATT
droVir3	scaffold_12855:1227223-1227391 +	1	TAATATTTTTTC-------------AAACGTGTTCA-G--------------------------TGTCGCCATCTTGCGGCACATACACAC----ACATTCAGA--CAAGATGTCACACGGACGTACGAAGA-GAACTGTCA-----GT-GTGTTTTGTGTGCCGTAGTGTGG---AGT--GTA-AATTTGTTGCGTCACTAGAAAAGTTCAACTGT-TGAAGGAAATC
droMoj3	scaffold_6540:26974787-26974936 +	1	TAACATTTTTTC-------------AAACGTGTTCA-AT--------------------------GTCGCCATCTTGCGGCTCACGCACAC----ACTCAT--G--CAAGATGTCACACGGGCGTATGAAGA-GAACTGTCA-----GT-GTT-----------A----------CTGT--GTG-AAGTCGTTGCGTCACTAGAAAAGTTCAACGATTTGAAGAAAATT
droGri2	scaffold_15245:5068344-5068468 +	2	-G-C-------G-------------ACAAGTGGTTGACTGCACCTGCACCCTCCCAA-------------------CAGACACACTCACAC----ACACAC----ACA---CAAC------------------------CCTCTGTGTGTGTGC---------AAGTGTGTGTGTGTGTGTGTC-AAA-CGCAGCA--ACTGCTGAAGTTT---------------AAC

[View All Possible Orthologs]

Original 12-way multiz alignment with reads super-imposed

Species

Alignment

dm3

TGCG----------AAACGT----------------GTTTGATAATGCG---CCGCCATCTTGCGGCACACTCGCACACA----CACA----------------------------CGTGTGCCA------------------TTCTGGTTTTGCAGTGGTGTGCGTGTGT-----GCCTC----GAGTCGTTGCGTCACTGGAAA---AGTTA-----------GAAAATC

Size

Hit Count

Total Norm

droSim1

TGCG----------AAACGT----------------GTTTGATAATGCG---CCGCCATCTTGCGGCACACTCGCACACA----CACA----------------------------CGTGTGCCA------------------GGCTGGTTTTGCAGTGGTGTGCGTGTGT-----GCCTC----GAGTCGTTGCGTCACTGGAAA---AGTTA-----------GAAAATC	Size	Hit Count	Total Norm	V044 Embryo	M023 Head	M024 Male body	M025 Embryo
...........................................................................................................................................................AGTGGTGTGCGTGTGT-----GCCTC----G..............................................	22	1	8.00	8.00	0.00	0.00	0.00
.........................................................................................................................................................................GT-----ACCTx----GAGTCGTTGCGTC..................................	19	1	3.00	0.00	0.00	3.00	0.00
..........................................................................................................................................................................T-----GCCTC----GAGTCGTTGCGTCAC................................	21	1	3.00	0.00	2.00	0.00	1.00
.........................................................................................................................................................................GT-----ACCTx----GAGTCGTTGCGTCA.................................	20	1	2.00	0.00	0.00	2.00	0.00
...............................................................CGGCACACTCGCACACA----CACA----------------------------C...................................................................................................................	22	1	2.00	0.00	2.00	0.00	0.00
....................................................................................................................CGTGAGACA------------------GGCTGGTTT................................................................................	18	1	2.00	2.00	0.00	0.00	0.00
...............................................................................A----CACA----------------------------CGTGTGCCA------------------GGCTG....................................................................................	19	1	2.00	0.00	0.00	0.00	2.00
...........................................................................................................................................................AGTGGTGTGCGTGTGT-----GCCT....................................................	20	1	1.00	1.00	0.00	0.00	0.00
..................................................................................................................................................................TGCGTGTGT-----GCCTC----GAGTCGT........................................	21	1	1.00	1.00	0.00	0.00	0.00
.........................................................................................................................................................................GT-----GCCTC----GAGTCGTTGCGTCACT...............................	23	1	1.00	0.00	0.00	0.00	1.00
.....................................................................................................................................................................................................CACTGGAAA---AGTTA-----------GAAAATC	21	1	1.00	0.00	1.00	0.00	0.00
..........................................................................................................................................................CAGTGGTGTGCGTGTGT-----GCC.....................................................	20	1	1.00	0.00	1.00	0.00	0.00
..........................................................................................................................................................CAGTGGTGTGCGTGTGT-----GCCTC----G..............................................	23	1	1.00	1.00	0.00	0.00	0.00
...............................................................CGGCACACTCGCACACA----CACA----------------------------CGTGTGCC............................................................................................................	29	1	1.00	0.00	1.00	0.00	0.00
.........................................................................................................................................................................GT-----GCCTC----GAGTCGTTGCGTCACTGGAAA---.......................	28	1	1.00	0.00	0.00	0.00	1.00
...........................................................................................................................CA------------------GGCTGGTTTTGCAGTGGTGTGC...................................................................	24	1	1.00	1.00	0.00	0.00	0.00
...................................................................................................................................................................GCGTGTGT-----GTCTC----GTGTC..........................................	18	1	1.00	0.00	0.00	0.00	1.00
...........................................................................................................................................................AGTxGTGTGTGTGTGT-----GCCT....................................................	19	1	1.00	1.00	0.00	0.00	0.00
.......................................................................................................................................................TTGCAGTGGTATGTGTGT...............................................................	18	1	1.00	1.00	0.00	0.00	0.00

droSec1

TGCG----------AAACGT----------------GTTTGATAATGCG---CCGCCATCTTGCGGCACACTCGCACACACACACACA----------------------------CGTGTGCCA------------------GGCTGGTTTTGCAGTGGTTTGCGTGTGT-----GCCTC----AAGTCGTTGCGTCACTGAAAA---AGTTA-----------GAAAATC	Size	Hit Count	Total Norm	V113 Male body	V114 Embryo	V115 Head
...........................................................................................................................................................AGTGGTTTGCGTGTGT-----GCCTC----A..............................................	22	1	2.00	0.00	1.00	1.00
..........................................................................................................................................................CAGTGGTTTGCGTGTGT-----GCCT....................................................	21	1	2.00	2.00	0.00	0.00
.....................................................................................................................................................................GTGTGT-----GCCTC----AAGTCGTTGC.....................................	21	1	1.00	0.00	1.00	0.00
..................................................................CACACACACACACACACACA..................................................................................................................................................	20	6	0.17	0.00	0.00	0.17
................................................................................................................................................................TTTGCGTGTGT-----GCCTC----AAGTCGC........................................	23	1	1.00	0.00	1.00	0.00
................................................................................................................................................................TTTGCGTGTGT-----GCCTC----AAGTC..........................................	21	1	1.00	0.00	0.00	1.00
..........................................................................................................................................................................................AGTCGTTGCGTCACTGAA............................	18	1	1.00	0.00	1.00	0.00
..................................................................................................................................................................TGCGTGTGT-----GCCTC----AAGTCG.........................................	20	1	1.00	0.00	1.00	0.00
...................................................................ACACACACACACACACACA..................................................................................................................................................	19	7	0.14	0.00	0.00	0.14
............................................................................................................................................................GTGGTTTGCGTGTGT-----GCCTC----A..............................................	21	1	1.00	0.00	0.00	1.00
.......................................................................................................................................................................GTGT-----GCCTC----CAGTCGTTG......................................	18	1	1.00	0.00	1.00	0.00
....................................................................CACACACACACACACACACA----------------------------....................................................................................................................	20	6	0.17	0.00	0.00	0.17
......................................................................................................................................................................TGTGT-----GCCTC----AAGTCGTTGAGTC..................................	23	1	1.00	1.00	0.00	0.00
....................................................................................................................................................GTTTTGCAGTGGTTTGCGT.................................................................	19	1	1.00	0.00	1.00	0.00
..........................................................................CACACACACACACA----------------------------CGAGTGC.............................................................................................................	21	2	0.50	0.00	0.50	0.00
...................................................................................................................................................GGTTTTGCAGTGGTTTGC...................................................................	18	1	1.00	0.00	1.00	0.00
..................................................................................................................................................................TGCGTGTGT-----GCCTC----AAGTCGT........................................	21	1	1.00	0.00	0.00	1.00
........................................................................................................................................................TGCAGxGGTGTGCGTGTGT-----........................................................	18	1	1.00	0.00	0.00	1.00
..................................................................CACACACACACACACACACAC.................................................................................................................................................	21	5	0.20	0.00	0.00	0.20
.....................................................................ACACACACACACACACACA----------------------------....................................................................................................................	19	7	0.14	0.00	0.00	0.14
......................................................................................................................TGTGCCA------------------GGCTGGTTTTGCAGTGGT.......................................................................	25	1	1.00	0.00	0.00	1.00
......................................................................................................................................................................TGTGT-----GCCTC----AAGTCGTTGCGT...................................	22	1	1.00	0.00	0.00	1.00
................................................................................................................................................................TTTGCGTGTGT-----GCCTT----AAGTCC.........................................	22	1	1.00	0.00	1.00	0.00
............................................................................................................................................................GTGGTTTGCGTGTGT-----GCCTC----AAGT...........................................	24	1	1.00	0.00	1.00	0.00
...................................................................................................................................................GGTTTTGCAGTGGTTTGCGTGT...............................................................	22	1	1.00	0.00	1.00	0.00
...............AACGT----------------GTTTGATAATGCG---C...................................................................................................................................................................................	19	1	1.00	0.00	1.00	0.00
....................................................................................CACA----------------------------CGTCTGCCA------------------GGCTG....................................................................................	18	1	1.00	0.00	1.00	0.00
....................................................................CACACACACACACACACACA----------------------------C...................................................................................................................	21	5	0.20	0.00	0.00	0.20
..................................................................CACACACACACACACACACACA----------------------------C...................................................................................................................	23	3	0.33	0.33	0.00	0.00
...............................................................CGGCACACTCGCACACACACACAC.................................................................................................................................................	24	1	1.00	0.00	1.00	0.00
....................................................................................................................................................................................C----AAGTCGTTGCGTCACTGAA............................	20	1	1.00	0.00	0.00	1.00

droYak2

TGCG----------AAACGT----------------GTTTGAAAATCCG---TCGCCATCTTGCGGCACACTCA--CACA----CACA----------------------------CGTGTGCCA------------------ATATGGTT-TGCAGTGGTGTGCGTGTG-------CCTC----GAGTCGTTGCGTCACTGGAAA---AGTCA-----------GAAAATC	Size	Hit Count	Total Norm	V046 Embryo	V052 Head	V120 Male body	V058 Head	M026 Head
..........................................................................................................................................................CAGTGGTGTGCGTGTG-------CCTC----GAG............................................	23	1	7.00	2.00	1.00	3.00	1.00	0.00
.............................................................TGCGGCACACTCA--CACA----CACA----------------------------C...................................................................................................................	22	1	4.00	0.00	0.00	0.00	0.00	4.00
.............................................................TGCGGCACACTCA--CACA----CACA----------------------------CGTGT...............................................................................................................	26	1	2.00	0.00	0.00	0.00	0.00	2.00
.................................................................................................................................................................GTGCGTGTG-------CCTC----GAGTCGTTGCGTCACT...............................	29	1	1.00	0.00	0.00	1.00	0.00	0.00
...........................................................................................................................CA------------------ATATGGTT-TGCAGTGGT.......................................................................	19	1	1.00	0.00	0.00	1.00	0.00	0.00
..........................................................................................................................................................CAGTGGTGTGCGTGTG-------CCTC----GA.............................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
..................................................................CACACACA--CACA----CACA----------------------------CATGT...............................................................................................................	21	1	1.00	0.00	0.00	1.00	0.00	0.00
..........................................................................................................................CCA------------------ATATGGTT-TGCAGTGGTGTGCGT.................................................................	26	1	1.00	0.00	0.00	1.00	0.00	0.00
..........................................................................................................................................................CAGGGGTGTGCGTGTG-------CCTC----GAG............................................	23	1	1.00	0.00	0.00	1.00	0.00	0.00
...........................................................................................................................................................AGTGGTGTGCGTGTG-------CCTC----GAG............................................	22	1	1.00	0.00	0.00	0.00	1.00	0.00
..................................................................CACACTCA--CACA----CAGA----------------------------CGCGTGC.............................................................................................................	23	1	1.00	0.00	0.00	1.00	0.00	0.00
......................................................................................................................................................T-TGCAGTGGTGTGCGTGTG-------CCT....................................................	22	1	1.00	0.00	1.00	0.00	0.00	0.00
.................................................................................................................................................................GTGCGTGTG-------CCTC----GAGTCGTTGCGTC..................................	26	1	1.00	0.00	0.00	1.00	0.00	0.00
.............................................................TGCGGCACACTCA--CACA----CACA----------------------------CG..................................................................................................................	23	1	1.00	1.00	0.00	0.00	0.00	0.00
..........................................................................................................................................................CAGTGGTGTGCGTGTG-------CCT....................................................	19	1	1.00	0.00	0.00	1.00	0.00	0.00
....................................................................CACTCA--CACA----CAGA----------------------------CGCGTGC.............................................................................................................	21	1	1.00	0.00	1.00	0.00	0.00	0.00

droEre2

TGCA----------AAACGT----------------GTTGGAAAATTCG---CCGCCATCTTGCGGCACACACA----CA----CACA----------------------------CGTGTGCCA------------------GTCTGGTT-TGCAGTGGTGTGCGTGTGG-----GCCTC----GAGTCGTTGCGTCACTGGAAA---AGTCC-----------GAAAATC	Size	Hit Count	Total Norm	V040 Embryo	V060 Head	V047 Embryo	V108 Head
...........................................................................................................................................................AGTGGTGTGCGTGTGG-----GCCTC----G..............................................	22	1	4.00	0.00	0.00	0.00	4.00
...........................................................................................................................................................AGTGGTGTGCGTGTGG-----GCCT....................................................	20	1	4.00	0.00	0.00	0.00	4.00
...........................................................................................................................................................AGTGGTGTGCGTGTGG-----GCCTC----...............................................	21	1	2.00	0.00	0.00	0.00	2.00
..................................................................CACACACA----CA----TACA----------------------------CGTAT...............................................................................................................	19	1	1.00	0.00	0.00	1.00	0.00
..........................................................................................................................................................CAGTGGTGTGCGTGTGG-----GCCT....................................................	21	1	1.00	0.00	0.00	0.00	1.00
..................................................................................................................................................................TGCGTGTGG-----GCCTC----GAGTC..........................................	19	1	1.00	1.00	0.00	0.00	0.00
.........................................................................................................................................................GCAGTGGTGTGCGTGTGG-----GCCTC----G..............................................	24	1	1.00	0.00	0.00	0.00	1.00
.......................................................................................................................................................................GTGG-----GCCTC----GAGTCGTTGC.....................................	19	1	1.00	0.00	0.00	0.00	1.00
...........................................................................................................................................................AGTGGTGTGCGTGTGG-----GCC.....................................................	19	1	1.00	0.00	0.00	0.00	1.00
..................................................................................................................................................................CGCGTGTGG-----GCCTC----GAGTCGTTT......................................	23	1	1.00	0.00	0.00	0.00	1.00
..........................................................................................................................CCA------------------GTCTGGTT-TGCAGTGGTGTGC...................................................................	24	1	1.00	0.00	0.00	0.00	1.00
......................................................................................................................................................................TGTGG-----GCCTC----GAGTCGTTGCGTCAC................................	25	1	1.00	0.00	0.00	0.00	1.00

droAna3

CTCA----------AAACGT----------------GTTCAA-----TGGAATCGCCATCTTGCGGCTCACACA----------CACA------------------------------TGTG-------------------------------ACAGTTGTTCGTGCGTGT-----GTCTGG---GAGTCGTTGCGTCACTGAGAA---AGTCG-----------GAAAAT-	Size	Hit Count	Total Norm	V105 Male body	V106 Head	V055 Unknown	V039 Embryo
........................................................................................................................................................................................................TGAGAG---TGTCG-----------GAAAAT-	17	1	1.00	0.00	0.00	1.00	0.00
...................................................................................................................................................................GTGCGTGT-----GTGTGT---GAGT...........................................	18	5	0.20	0.20	0.00	0.00	0.00
..........................................................................................................................................................CAGTTGTTCGTGCGTGT-----GTCTGG---GA.............................................	25	1	1.00	1.00	0.00	0.00	0.00

dp4

TGTA---------------CATTTTCTCGAAAACGTGTCGAA-----TG---TCGCCATCTTGCGGgt-gtgtgtgtGtg----tgtg----------------------------tgtgtgtTGTGACGAGAGGAATTGCCAGTGCT------CAATAGTGTGCCTGTGT-----G--TC----GAGACGTTGCGTCACTGAAAA---AGTCGAACAGC--AAAGTAAATT	Size	Hit Count	Total Norm	V112 Male body	V043 Embryo	V051 Head	M022 Male body
.................................................................TGT-GTGTGTGTGTG----TGTG----------------------------TGTGTG..............................................................................................................	24	17	1.47	0.24	0.00	1.24	0.00
...................................................................T-GTGTGTGTGTG----TGTG----------------------------TGTGTGTG............................................................................................................	24	17	1.47	0.24	0.00	1.24	0.00
..................................................................GT-GTGTGTGTGTG----TGTG----------------------------TGTGTGTG............................................................................................................	25	15	0.53	0.07	0.00	0.47	0.00
................................................................GTGT-GTGTGTGTGTG----TGTG----------------------------TGTGTG..............................................................................................................	25	15	0.53	0.07	0.00	0.47	0.00
..................................................................GT-GTGTGTGTGTG----TGTG----------------------------TGTGTG..............................................................................................................	23	20	0.30	0.00	0.00	0.30	0.00
.....................................................................GTGTGTGTGTG----TGTG----------------------------TGTGTGTG............................................................................................................	23	20	0.30	0.00	0.00	0.30	0.00
.................................................................TGT-GTGTGTGTGTG----TGTG----------------------------TGTGTGT.............................................................................................................	25	13	0.46	0.08	0.00	0.38	0.00
................................................................GTGT-GTGTGTGTGTG----TGTG----------------------------TGTG................................................................................................................	23	20	0.30	0.00	0.00	0.30	0.00
..................................................................GT-ACGTGTGTGTG----TGTG----------------------------TG..................................................................................................................	19	26	0.19	0.08	0.08	0.04	0.00
.......................................................................GTACGTGTG----TGTG----------------------------TGTGTG..............................................................................................................	19	26	0.19	0.08	0.08	0.04	0.00
.....................................................................GTACGTGTGTG----TGTG----------------------------TGT.................................................................................................................	18	29	0.17	0.00	0.17	0.00	0.00
.......................................................................GTACGTGTG----TGTG----------------------------TGTGT...............................................................................................................	18	29	0.17	0.00	0.17	0.00	0.00
.........................................................................GTACGTG----TGTG----------------------------TGTGTGT.............................................................................................................	18	29	0.17	0.00	0.17	0.00	0.00
.....................................................................GTACGTGTGTG----TGTG----------------------------TGTG................................................................................................................	19	26	0.19	0.08	0.08	0.04	0.00
..................................................................GT-ACGTGTGTGTG----TGTG----------------------------T...................................................................................................................	18	29	0.17	0.00	0.17	0.00	0.00
......................................................................TGTGTGTGTG----TGTG----------------------------TGTGTGTG............................................................................................................	22	21	0.19	0.00	0.00	0.19	0.00
.................................................................TGT-GTGTGTGTGTG----TGTG----------------------------TGTG................................................................................................................	22	21	0.19	0.00	0.00	0.19	0.00
...................................................................T-GTGTGTGTGTG----TGTG----------------------------TGTGTGTT............................................................................................................	24	13	0.31	0.00	0.08	0.23	0.00
..........................................................................TGTGTG----TATG----------------------------TGTGTTTTGT..........................................................................................................	20	1	4.00	4.00	0.00	0.00	0.00
...................................................................T-GTGTGTGTGTG----TGTG----------------------------TGTGTG..............................................................................................................	22	21	0.19	0.00	0.00	0.19	0.00
..........................................................................TTTGTG----TGTG----------------------------TGTGTGTG............................................................................................................	18	37	0.08	0.03	0.03	0.03	0.00
........................................................................TCTGTGTG----TGTA----------------------------TGTGTGTT............................................................................................................	20	1	3.00	3.00	0.00	0.00	0.00
......................................................................TTTGTGTGTG----TGTG----------------------------TGTG................................................................................................................	18	37	0.08	0.03	0.03	0.03	0.00
...................................................................T-TTGTGTGTGTG----TGTG----------------------------TG..................................................................................................................	18	37	0.08	0.03	0.03	0.03	0.00
........................................................................TGTGTGTG----TGTG----------------------------TGTGTGT.............................................................................................................	19	27	0.11	0.04	0.00	0.07	0.00
.................................................................TTT-GTGTGTGTGTG----TGTG----------------------------....................................................................................................................	18	37	0.08	0.03	0.03	0.03	0.00
.....................................................................................GTG----------------------------TGTGTGTTGTGAGGG.....................................................................................................	18	1	3.00	3.00	0.00	0.00	0.00
..................................................................GT-GTGTGTGTGTG----TGTG----------------------------TGTGTGTGG...........................................................................................................	26	13	0.23	0.15	0.00	0.08	0.00
........................................................................TTTGTGTG----TGTG----------------------------TGTGTG..............................................................................................................	18	37	0.08	0.03	0.03	0.03	0.00
.................................................................TGT-GTGTGTGTGTG----TGTG----------------------------TGTGTGTT............................................................................................................	26	14	0.21	0.00	0.00	0.21	0.00
......................................................................TGTCTGTGTG----TGTA----------------------------TGTGTG..............................................................................................................	20	20	0.15	0.15	0.00	0.00	0.00
...................................................................T-GTGTGTGTGTG----TGTG----------------------------TGT.................................................................................................................	19	27	0.11	0.04	0.00	0.07	0.00
......................................................................TGTGTGTGTG----TGTG----------------------------TGTGT...............................................................................................................	19	27	0.11	0.04	0.00	0.07	0.00
...................................................................T-GTCTGTGTGTG----TATG----------------------------TGTG................................................................................................................	20	20	0.15	0.15	0.00	0.00	0.00
...................................................................T-GTGTGTGTGTG----TGTG----------------------------TGTGTGTGTT..........................................................................................................	26	14	0.21	0.00	0.00	0.21	0.00
.................................................................TGT-GTGTGTGTGTG----TGTG----------------------------T...................................................................................................................	19	27	0.11	0.04	0.00	0.07	0.00

droPer1

TGTA---------------CATTTTCTCGAAAACGTGTCGAA-----TG---TCGCCATCTTGCGGgt-gtgtgtgtGtg----tgtg----------------------------tgtgtgtTGTGACGAGAGGAATTGCCAGTGCT------CAATAGTGTGCCTGTGT-----G--TC----GAGACGTTGCGTCACTGAAAA---AGTCGAACAGC--AAAGTAAATT	Size	Hit Count	Total Norm	V111 Male body	V042 Embryo	V050 Head	V057 Head	M021 Embryo
......................................................................TGTTTGTTTG----TGTG----------------------------TGTGTGT.............................................................................................................	21	18	1.44	0.89	0.06	0.28	0.22	0.00
...................................................................T-GTTTGTTTGTG----TGTG----------------------------TGTGT...............................................................................................................	21	18	1.44	0.89	0.06	0.28	0.22	0.00
.....................................................................GTGTGTGTGTG----TGTG----------------------------TGTGT...............................................................................................................	20	32	0.47	0.47	0.00	0.00	0.00	0.00
.......................................................................GTGTGTGTG----TGTG----------------------------TGTGTGT.............................................................................................................	20	32	0.47	0.47	0.00	0.00	0.00	0.00
..................................................................GT-GTGTGTGTGTG----TGTG----------------------------TGT.................................................................................................................	20	32	0.47	0.47	0.00	0.00	0.00	0.00
................................................................GTGT-GTGTGTGTGTG----TGTG----------------------------T...................................................................................................................	20	32	0.47	0.47	0.00	0.00	0.00	0.00
.....................................................................GTGCGTGTGTG----TGTG----------------------------TGTGC...............................................................................................................	20	26	0.46	0.12	0.35	0.00	0.00	0.00
..................................................................GT-GCGTGTGTGTG----TGTG----------------------------TGC.................................................................................................................	20	26	0.46	0.12	0.35	0.00	0.00	0.00
.......................................................................GTGCGTGTG----TGTG----------------------------TGTGTGC.............................................................................................................	20	26	0.46	0.12	0.35	0.00	0.00	0.00
.....................................................................GTGTGTGTGTG----TGTG----------------------------TGT.................................................................................................................	18	41	0.22	0.17	0.05	0.00	0.00	0.00
................................................................GTGT-GTGTGTGTGTG----TGT.................................................................................................................................................	18	41	0.22	0.17	0.05	0.00	0.00	0.00
..................................................................GT-GTGTGTGTGTG----TGTG----------------------------TGTG................................................................................................................	21	29	0.31	0.31	0.00	0.00	0.00	0.00
.........................................................................GTGTGTG----TGTG----------------------------TGTGTGT.............................................................................................................	18	41	0.22	0.17	0.05	0.00	0.00	0.00
................................................................GTGT-GTGTGTGTGTG----TGTG----------------------------TG..................................................................................................................	21	29	0.31	0.31	0.00	0.00	0.00	0.00
.......................................................................GTGTGTGTG----TGTG----------------------------TGTGT...............................................................................................................	18	41	0.22	0.17	0.05	0.00	0.00	0.00
.....................................................................GTGTGTGTGTG----TGTG----------------------------TGTGTG..............................................................................................................	21	29	0.31	0.31	0.00	0.00	0.00	0.00
.......................................................................GTGTGTGTG----TGTG----------------------------TGTGTGTG............................................................................................................	21	29	0.31	0.31	0.00	0.00	0.00	0.00
..................................................................GT-GTGTGTGTGTG----TGTG----------------------------T...................................................................................................................	18	41	0.22	0.17	0.05	0.00	0.00	0.00
.....................................................................GTGCGTGTGTG----TGTG----------------------------TGTG................................................................................................................	19	42	0.19	0.10	0.10	0.00	0.00	0.00
.......................................................................GTGCGTGTG----TGTG----------------------------TGTGT...............................................................................................................	18	26	0.31	0.04	0.27	0.00	0.00	0.00
.....................................................................GTGCGTGTGTG----TGTG----------------------------TGT.................................................................................................................	18	26	0.31	0.04	0.27	0.00	0.00	0.00
..............................................................GTGCGT-GTGTGTGTGTG----TG..................................................................................................................................................	19	42	0.19	0.10	0.10	0.00	0.00	0.00
.......................................................................GTGCGTGTG----TGTG----------------------------TGTGTG..............................................................................................................	19	42	0.19	0.10	0.10	0.00	0.00	0.00
............................................................GTGCGTGT-GTGTGTGTGTG----....................................................................................................................................................	19	42	0.19	0.10	0.10	0.00	0.00	0.00
..................................................................GT-GCGTGTGTGTG----TGTG----------------------------TG..................................................................................................................	19	42	0.19	0.10	0.10	0.00	0.00	0.00
..................................................................GT-GCGTGTGTGTG----TGTG----------------------------T...................................................................................................................	18	26	0.31	0.04	0.27	0.00	0.00	0.00
.........................................................................GTGCGTG----TGTG----------------------------TGTGTGT.............................................................................................................	18	26	0.31	0.04	0.27	0.00	0.00	0.00
................................................................GTGC-GTGTGTGTGTG----TGTG----------------------------....................................................................................................................	19	42	0.19	0.10	0.10	0.00	0.00	0.00
.........................................................................GTGCGTG----TGTG----------------------------TGTGTGTG............................................................................................................	19	42	0.19	0.10	0.10	0.00	0.00	0.00
...................................................................T-GTGTGTGTGTG----TGTG----------------------------TGTG................................................................................................................	20	32	0.22	0.19	0.00	0.03	0.00	0.00
........................................................................TGTGTGTG----TGTG----------------------------TGTGTGTG............................................................................................................	20	32	0.22	0.19	0.00	0.03	0.00	0.00
........................................................................TGTGTGTG----TGTG----------------------------TGTGTG..............................................................................................................	18	39	0.18	0.08	0.00	0.08	0.03	0.00
...................................................................T-GTGTGTGTGTG----TGTG----------------------------TG..................................................................................................................	18	39	0.18	0.08	0.00	0.08	0.03	0.00
...................................................................T-GTTTGTTTGTG----TGTG----------------------------TGTG................................................................................................................	20	23	0.30	0.17	0.04	0.00	0.09	0.00
..........................................................................TGTGTG----TGTG----------------------------TGTGTGTG............................................................................................................	18	39	0.18	0.08	0.00	0.08	0.03	0.00
......................................................................TGTGTGTGTG----TGTG----------------------------TGTG................................................................................................................	18	39	0.18	0.08	0.00	0.08	0.03	0.00
......................................................................TGTGTGTGTG----TGTG----------------------------TGTGTGT.............................................................................................................	21	29	0.24	0.17	0.07	0.00	0.00	0.00
.................................................................TGT-GTGTGTGTGTG----TGTG----------------------------TG..................................................................................................................	20	32	0.22	0.19	0.00	0.03	0.00	0.00
.................................................................TGT-GTGTGTGTGTG----TGTG----------------------------....................................................................................................................	18	39	0.18	0.08	0.00	0.08	0.03	0.00
.................................................................TGT-GTGTGTGTGTG----TGTG----------------------------TGT.................................................................................................................	21	29	0.24	0.17	0.07	0.00	0.00	0.00
...................................................................T-GTGTGTGTGTG----TGTG----------------------------TGTGT...............................................................................................................	21	29	0.24	0.17	0.07	0.00	0.00	0.00
......................................................................TGTGTGTGTG----TGTG----------------------------TGTGTG..............................................................................................................	20	32	0.22	0.19	0.00	0.03	0.00	0.00
......................................................................TGTTTGTTTG----TGTG----------------------------TGTGTG..............................................................................................................	20	23	0.30	0.17	0.04	0.00	0.09	0.00
.................................................................TGT-GTGTGTGTGTG----TGTG----------------------------TGTGTG..............................................................................................................	24	20	0.25	0.15	0.00	0.05	0.05	0.00
........................................................................TGTGTGTG----TGTG----------------------------TGTGTGT.............................................................................................................	19	36	0.14	0.14	0.00	0.00	0.00	0.00
..................................................................GT-GCGTGTGTGTG----TGTG----------------------------TGCG................................................................................................................	21	23	0.22	0.17	0.04	0.00	0.00	0.00
...................................................................T-GTGTGTGTGTG----TGTG----------------------------TGT.................................................................................................................	19	36	0.14	0.14	0.00	0.00	0.00	0.00
......................................................................TGTGTGTGTG----TGTG----------------------------TGTGT...............................................................................................................	19	36	0.14	0.14	0.00	0.00	0.00	0.00
..........................................................................TGTGTG----TGTA----------------------------TGTGTGTTTT..........................................................................................................	20	2	2.50	2.00	0.00	0.00	0.50	0.00
........................................................................TGTGTGTG----TATG----------------------------TGTGTTTT............................................................................................................	20	2	2.50	2.00	0.00	0.00	0.50	0.00
.....................................................................GTGCGTGTGTG----TGTG----------------------------TGTGCG..............................................................................................................	21	23	0.22	0.17	0.04	0.00	0.00	0.00
...................................................................T-GTGTGTGTGTG----TGTG----------------------------TGTGTGTG............................................................................................................	24	20	0.25	0.15	0.00	0.05	0.05	0.00
.................................................................TGT-GTGTGTGTGTG----TGTG----------------------------T...................................................................................................................	19	36	0.14	0.14	0.00	0.00	0.00	0.00
......................................................................TGTGTGTGTG----TGTG----------------------------TGTGTGTG............................................................................................................	22	26	0.15	0.15	0.00	0.00	0.00	0.00
.................................................................TGT-GTGTGTGTGTG----TGTG----------------------------TGTG................................................................................................................	22	26	0.15	0.15	0.00	0.00	0.00	0.00
.............................................................................................................................................................................................CGTTGCGTCACTGAAAA---AGTCGAAC...............	25	1	4.00	0.00	0.00	0.00	0.00	4.00
...................................................................T-GTGTGTGTGTG----TGTG----------------------------TGTGTG..............................................................................................................	22	26	0.15	0.15	0.00	0.00	0.00	0.00
......................................................................TGTGTGTGTG----TGTx----------------------------TGTCTGT.............................................................................................................	20	55	0.07	0.07	0.00	0.00	0.00	0.00
...................................................................T-GTGTGTGTGTG----TxTG----------------------------TCTGT...............................................................................................................	20	55	0.07	0.07	0.00	0.00	0.00	0.00
................................................................................................................................................................................G--TC----GAGACGTTGCGTCACTGA.............................	21	1	4.00	0.00	0.00	0.00	0.00	4.00
..................................................................GT-GTGTGTGTGTG----xGTG----------------------------TGTGTC..............................................................................................................	22	35	0.11	0.11	0.00	0.00	0.00	0.00
.........................................................................GTGTGTG----TATG----------------------------TGTGTTTTG...........................................................................................................	20	2	2.00	1.50	0.00	0.50	0.00	0.00
...........................................................................GTGTG----TGTA----------------------------TGTGTGTTTTG.........................................................................................................	20	2	2.00	1.50	0.00	0.50	0.00	0.00
.......................................................................GTGTGTGTG----TTTG----------------------------TGTGTA..............................................................................................................	19	27	0.11	0.11	0.00	0.00	0.00	0.00
.........................................................................GTGTGTG----TGTG----------------------------TTTGTGGT............................................................................................................	19	3	1.00	1.00	0.00	0.00	0.00	0.00
.................................................................CGT-GCGTGTGTGTG----TGTG----------------------------TG..................................................................................................................	20	29	0.10	0.10	0.00	0.00	0.00	0.00
..................................................................GT-TTGTTTGTGTG----TGTG----------------------------TGT.................................................................................................................	20	22	0.14	0.14	0.00	0.00	0.00	0.00
.....................................................................GTTTGTTTGTG----TGTG----------------------------TGTGT...............................................................................................................	20	22	0.14	0.14	0.00	0.00	0.00	0.00
...........................................................................GTGTG----CGTG----------------------------TGTGTGTGGT..........................................................................................................	19	3	1.00	1.00	0.00	0.00	0.00	0.00
...............................................................CGAGT-GTGTGTGTGTA----TGT.................................................................................................................................................	19	4	0.75	0.75	0.00	0.00	0.00	0.00
.........................................................................GTGTGTG----TGTT----------------------------TGTGTGTA............................................................................................................	19	27	0.11	0.11	0.00	0.00	0.00	0.00
.................................................................................................................................................................GTGCCTGTGT-----G--TC----GAGACGTTGCGTCACT...............................	29	1	3.00	0.00	0.00	0.00	0.00	3.00
..............................................................................................................................................................AGTGTGCCTGTGT-----G--TC----GAGACGTTGC.....................................	26	1	3.00	0.00	0.00	0.00	0.00	3.00
.....................................................................GTGTTTGTGTG----TGTG----------------------------TTTGTG..............................................................................................................	21	20	0.15	0.15	0.00	0.00	0.00	0.00
.........................................................................GTGTGTG----TATG----------------------------TGTGTTTT............................................................................................................	19	2	1.50	1.00	0.00	0.00	0.50	0.00
.....................................................................GTGTGTGTGCG----TGTG----------------------------TGAGTG..............................................................................................................	21	20	0.15	0.15	0.00	0.00	0.00	0.00
.....................................................................GTATCTGTGTG----TGTG----------------------------TGT.................................................................................................................	18	28	0.11	0.11	0.00	0.00	0.00	0.00
...........................................................CGTGCGTGT-GTGTGTGTGTG----....................................................................................................................................................	20	29	0.10	0.10	0.00	0.00	0.00	0.00
.....................................................................GTATGTGTATG----TGTG----------------------------TGT.................................................................................................................	18	27	0.11	0.04	0.00	0.00	0.00	0.07
.................................................................GGT-GTGTGTGTGTG----TGTG----------------------------T...................................................................................................................	19	24	0.13	0.13	0.00	0.00	0.00	0.00
................................................................GTGT-GTGTGTGTGTG----TGTG----------------------------AGT.................................................................................................................	22	30	0.10	0.10	0.00	0.00	0.00	0.00
..................................................................GT-GTGTGTGTTTG----TGTG----------------------------TA..................................................................................................................	19	27	0.11	0.11	0.00	0.00	0.00	0.00
.........................................................................GTATGTG----TATG----------------------------TGTGTGT.............................................................................................................	18	27	0.11	0.04	0.00	0.00	0.00	0.07
..................................................................GT-GTGTGTGTGTG----TGTG----------------------------TGAGT...............................................................................................................	22	30	0.10	0.10	0.00	0.00	0.00	0.00
..................................................................GT-GTGTGTGCGTG----TGTG----------------------------AGTG................................................................................................................	21	20	0.15	0.15	0.00	0.00	0.00	0.00
..................................................................GT-ATCTGTGTGTG----TGTG----------------------------T...................................................................................................................	18	28	0.11	0.11	0.00	0.00	0.00	0.00
.....................................................................................................................................................................................................CACTGAAAA---AGTCGAACAG.............	19	1	3.00	0.00	0.00	0.00	0.00	3.00
...........................................................................GTGTG----TGTG----------------------------TGTTTGTGGT..........................................................................................................	19	3	1.00	1.00	0.00	0.00	0.00	0.00
.....................................................................GTGTGTGTGTT----TGTG----------------------------TGTA................................................................................................................	19	27	0.11	0.11	0.00	0.00	0.00	0.00
......................................................................GGTGTGTGTG----TGTG----------------------------TGTGT...............................................................................................................	19	24	0.13	0.13	0.00	0.00	0.00	0.00
.........................................................................GTGTGCG----TGTG----------------------------TGTGTGGT............................................................................................................	19	3	1.00	1.00	0.00	0.00	0.00	0.00
..................................................................GT-GTTTGTGTGTG----TGTT----------------------------TGTG................................................................................................................	21	20	0.15	0.15	0.00	0.00	0.00	0.00
........................................................................GGTGTGTG----TGTG----------------------------TGTGTGT.............................................................................................................	19	24	0.13	0.13	0.00	0.00	0.00	0.00
...........................................................................GTGTG----TGTA----------------------------TGTGTGTTTT..........................................................................................................	19	2	1.50	1.00	0.00	0.00	0.50	0.00
...................................................................G-GTGTGTGTGTG----TGTG----------------------------TGT.................................................................................................................	19	24	0.13	0.13	0.00	0.00	0.00	0.00
.......................................................................GTATCTGTG----TGTG----------------------------TGTGT...............................................................................................................	18	28	0.11	0.11	0.00	0.00	0.00	0.00
.....................................................................GTGTGTGTGTG----TGTA----------------------------TGTGT...............................................................................................................	20	32	0.09	0.09	0.00	0.00	0.00	0.00
.......................................................................GTGTGTGTG----TGTG----------------------------TATGTGT.............................................................................................................	20	32	0.09	0.09	0.00	0.00	0.00	0.00
.......................................................................GTTTGTTTG----TGTG----------------------------TGTGTGT.............................................................................................................	20	22	0.14	0.14	0.00	0.00	0.00	0.00
...................................................................C-GTGCGTGTGTG----TGTG----------------------------TGTG................................................................................................................	20	29	0.10	0.10	0.00	0.00	0.00	0.00
..................................................................GT-GTGTGTGTGTG----TATG----------------------------TGT.................................................................................................................	20	32	0.09	0.09	0.00	0.00	0.00	0.00

droWil1

TGAA----------AAATGTATTTTATCT--A--------GAGATATTG---TCGCCATTTTGCGGCACTCACA----------CACA----------------------------CGTGTCACA------AGAGAACTGTCAAA------TTGTAGCTGTATGCGTGAG---------AC----CAGTCGTTGCGTCACAGCAAA---AGTTT-----------TCAAATT	Size	Hit Count	Total Norm	V117 Male body	V118 Embryo	V119 Head	M020 Head
...............CATGTATTTTATCT--A--------GAGATATT........................................................................................................................................................................................	23	1	1.00	0.00	1.00	0.00	0.00
........................................GAGATATTG---TCGCCATTTTGCGGCA....................................................................................................................................................................	25	1	1.00	0.00	1.00	0.00	0.00
.......................TTATCT--A--------GAGATATTG---TCGC................................................................................................................................................................................	20	1	1.00	0.00	1.00	0.00	0.00
..........................................................................................................................................TGTCGAA------TTGTGGCTGTATGC...................................................................	21	1	1.00	0.00	0.00	1.00	0.00
.......................................................................................A----------------------------CGTGTCACA------AGAGAACT.............................................................................................	18	1	1.00	0.00	1.00	0.00	0.00
..................................................................................................................................................................TGCGTGAG---------AC----CAGTCGTTGCG....................................	21	1	1.00	0.00	1.00	0.00	0.00
..........................TCT--A--------GAGATATTG---TCGCC...............................................................................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
...........................................................................................................................CA------AGAGAACTxTGAAA------TTG..............................................................................	18	1	1.00	0.00	1.00	0.00	0.00

droVir3

ACAG-ATGAGTGAAAATAATATTTTTTCA--AACGTGTTCAG-----TG---TCGCCATCTTGCGGCACATACACACACA----TTCA------G----ACAAGATGTCACACGGAC--GT------ACGAAGAGAACTGTCAGTGTGTTT-------TGTGTGCCGTAGTGTGGAGTGTA----AATTTGTTGCGTCACTAGAAA---AGTTCAACTGT-TGAAGGAAATC	Size	Hit Count	Total Norm	V116 Male body	V053 Unknown	V047 Embryo	M027 Male body	M028 Head
....................................................................................................................................................................................A----AATTTGTTGCGTCACTAGA............................	20	1	2.00	1.00	0.00	1.00	0.00	0.00
.......................................................................................................................................................................................................CTAGAAA---AGTTCAACTGT-T..........	19	1	1.00	0.00	1.00	0.00	0.00	0.00
.........................................................................................................................................................................................AATTTGTTGCGTCACTAGAAA---AG.....................	23	1	1.00	0.00	0.00	0.00	0.00	1.00
............................................................................................................CACACGGAC--GT------ACGAAGAGA................................................................................................	20	1	1.00	0.00	0.00	1.00	0.00	0.00
...............................................................................................................ACGGAC--GT------ACGAAGAGAACT.............................................................................................	20	1	1.00	0.00	0.00	0.00	1.00	0.00
...................................................................................................................................................GTTT-------TGTGTGCCGTAGTGTGG.........................................................	21	1	1.00	1.00	0.00	0.00	0.00	0.00
....................................................................................................................................................TTT-------TGTGTGCCTTAGTGTGGA........................................................	21	1	1.00	0.00	0.00	1.00	0.00	0.00
...................................................................................................................................................GTTT-------TGTGTGCCGTAGTGTGGA........................................................	22	1	1.00	0.00	0.00	1.00	0.00	0.00
............................................................................................................CACACGGAC--GT------ACGAAGAGAACTGTCAG........................................................................................	28	1	1.00	0.00	0.00	0.00	1.00	0.00
.............................................................................................................ACACGGAC--GT------ACGAAGAGAA...............................................................................................	20	1	1.00	0.00	0.00	0.00	0.00	1.00
.............................................................................................................ACACGGAC--GT------ACGAAGAGAACTG............................................................................................	23	1	1.00	0.00	0.00	0.00	0.00	1.00
..............................................................................................................CACGGAC--GT------ACGAAGAGAACTG............................................................................................	22	1	1.00	1.00	0.00	0.00	0.00	0.00
.............................................................................................................................................GAGTGTxTAT-------TGTGTGCCG.................................................................	18	1	1.00	0.00	0.00	1.00	0.00	0.00
.............................................................................................................ACACGGAC--GT------ACGAAGAGAACTGTCAC........................................................................................	27	1	1.00	0.00	0.00	0.00	1.00	0.00

droMoj3

AAAA-ACAAGTGAAAATAACATTTTTTCA--AACGTGTTCAA-----TG---TCGCCATCTTGCGGCTCACGCA--CACA----CTCA------T----GCAAGATGTCACACGGGC--GT------ATGAAGAGAACTGTCAGTGTT------------------ACT-------GTGTG----AAGTCGTTGCGTCACTAGAAA---AGTTCAACGATTTGAAGAAAATT	Size	Hit Count	Total Norm	V110 Male body	V056 Unknown	V049 Head	V041 Embryo
..............................................................................................................................................AGTGTT------------------GCT-------GTGTG----AGGTCGT........................................	21	1	1.00	1.00	0.00	0.00	0.00
.....................................................................................TCA------T----GCAAGATGTCACAC.......................................................................................................................	18	1	1.00	0.00	0.00	0.00	1.00
..................................................................................................................GGC--GT------TTGxAGAGAACTG............................................................................................	17	1	1.00	0.00	1.00	0.00	0.00

droGri2

GGAATATTAGTGAAAATATTATTTTCTCC--AACGTGTTCAA---TGTG---TCGCCATCTTGCGGgt-gtTGgtgtgtG----tgtgtgtgtgtgtgtg-tAGATGTCACACGGGCCCGT------ATGAAGAGAACTGTCAGTTT------GTGTCAGTGTGCGTGTG-------CTTT-ACTCTATTGTTGCGTCACAAGAAACTAAAA-----------AAGAAAATC	Size	Hit Count	Total Norm	V109 Male body
..........................................................................TGTGTG----TGTGTTTGTGTGT.......................................................................................................................................	19	41	0.07	0.07
..............................................................................TG----TGTGTGTGTTTGTGTG-T..................................................................................................................................	19	41	0.07	0.07
........................................................................TGTGTGTG----TGTTTGTGTGT.........................................................................................................................................	19	41	0.07	0.07
............................................................................TGTG----TGTGTGTGTGTGTGCG-TG.................................................................................................................................	22	34	0.09	0.09
............................................................................TGTG----TGTGTGTTTGTGTGT.....................................................................................................................................	19	41	0.07	0.07
............................................................................TGTG----TGTGTGTGTGTGTGTG-C..................................................................................................................................	21	18	0.17	0.17
..........................................................................TGTGTG----TGTGTGTGTGTGCGTG-...................................................................................................................................	22	34	0.09	0.09
..........................................................................TGTGTG----TGTGTGTGTGTGTGC.....................................................................................................................................	21	18	0.17	0.17
........................................................................TGTGTGTG----TGTGTGTGTGCGTG......................................................................................................................................	22	34	0.09	0.09

12-way Secondary Structure

	dm3	droSim1	droSec1	droYak2	droEre2	droAna3	dp4	droPer1	droWil1	droVir3	droMoj3	droGri2
RNAfold Image
UNAFold Image

20-way Secondary Structure

	dm3	droSim1	droSec1	droYak2	droEre2	droEug1	droBia1	droTak1	droEle1	droRho1	droFic1	droKik1	droAna3	droBip1	dp4	droPer1	droWil1	droVir3	droMoj3	droGri2
RNAfold Image
UNAFold Image